1. Field of the Invention
The present invention relates to the field of molecular biology and nucleic acid chemistry. More specifically, it relates to methods and reagents for detecting human immunodeficiency virus (HIV-1). The invention therefore has applications in the field of medicine generally, medical diagnostics specifically, and the field of molecular biology.
2. Description of Related Art
The invention of the polymerase chain reaction (PCR), a method for amplifying specific sequences of nucleic acids, makes possible the rapid detection of nucleic acids present in a sample in what was previously an undetectably low quantity (see U.S. Pat. Nos. 4,683,195; 4,683,202; and 4,965,188, each of which is incorporated herein by reference). A preferred method of detecting amplified nucleic acid is by hybridization with a sequence-specific oligonucleotide probe (see Saiki et al, 1986, Nature 324:163-166, incorporated herein by reference).
The use of PCR and probe hybridization to amplify and detect HIV-1 nucleic acid is reviewed in Kwok, 1992, Ann. Med. 24:211-214, and Coutlee et al., 1991, Mol. Cell. Probes 5:241-259, both incorporated herein by reference. PCR-based HIV-1 detection assays are described in, for example, U.S. Pat. Nos. 5,008,182 and 5,176,775, Kellogg and Kwok, 1990, in PCR Protocols: A Guide to Methods and Applications (ed. Innis et al., Academic Press, San Diego, Calif.):337-347, and Jackson et. al., 1991, AIDS 5:1463-1467, each incorporated herein by reference. In addition, reagents for the amplification and detection of HIV-1 are commercially available.
HIV-1 displays considerable genomic sequence variability not only between isolates from different individuals, but also between isolates from the same individual over time. Phylogenetic analysis of the nucleic acid sequences of HIV-1 gag and env genes has identified at least 5 subtypes, depending On the coding sequence considered (see Myers et al., 1993, Human Retrovirus and AIDS 1993, Los Alamos National Laboratory, Los Alamos, N. Mex., incorporated herein by reference). The most divergent HIV-1 have been identified in Africa. In particular, two divergent strains of HIV-1, designated ANT70 and MVP5180, were isolated from patients originating from Cameroon in West-Central Africa. Although the genomic organization of these isolates was similar to other HIV-1 subtypes, significant nucleotide sequence divergence was observed. The nucleic acid sequences of these isolates are available under accession numbers L20587 for ANT-70 and L20571 for MVP-5180. These new subtypes have been provisionally designated as subtype O.